Related Packages

  • VMD (with its plugins and script library) is closely tied to NAMD and is used for:
    • visualizing the initial structure and trajectory
    • assembling biomolecular aggregates
    • solvating the system in a membrane and/or water
    • building the molecular structure (PSF file)
    • visualizing and analyzing the trajectory
  • Tcl is used within NAMD and VMD to provide scripting capabilities.
  • FFTW 2.1.5 may be compiled into NAMD for better PME performance.
  • CHARMM may be useful for setup and analysis.
  • The CHARMM parameters are available for use with NAMD.
  • Find CHARMM docs and forums at www.charmm.org and other useful info at http://brooks.chem.lsa.umich.edu/charmm_docs/TSRI_docs-list.htm.
  • The Cornell et al. (AMBER) parameters are available in CHARMM format for use with NAMD.
  • The OPLS parameters are available in CHARMM format for use with NAMD. OPLS requires the vdwGeometricSigma option, see NamdAndOPLS on the NamdWiki.
  • Alchemify by Jérôme Hénin prepares files for alchemical free energy calculations.
  • namd_ti.pl Perl script for analysis of output files from thermodynamic integration method in Alchemical Free Energy Module of NAMD2.

Useful Scripts

Example Simulations